sQTLseekeR

sQTLseekeR is a R package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. Here, splicing patterns are modeled by the relative expression of the transcripts of a gene. For more information about the method and performance see article : Monlong, J. et al. Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat. Commun. 5:4698 doi: 10.1038/ncomms5698 (2014).

 

The latest version as well as more details on installation and usage can be found on sQTLseekeR github page.

New in sQTLseekeR 2.0 (2014-10-14) : New packaging available and maintained on GitHub.

New in sQTLseekeR-1-3 (2014-09-18) : Fix svQTL problem due to an updated version of 'vegan' package.

New in sQTLseekeR-1-2 (2014-06-18) : More extensive output: MaxDiff splicing ratios between groups and pair of transcripts that change the most.

New in sQTLseekeR-1-1 (2014-02-21) : 'vegan' package error catching when splicing dispersion and gene expression are too low.